Project name: be214f11cbf069c

Status: done

Started: 2026-06-03 06:36:44
Settings
Chain sequence(s) A: GIVEQCCTSICSLYQLENYCN
C: GIVEEQQCCTSICSLYQLENYCN
B: FVNQHLCGSHLVVEALYLVCGERGFFFYTPK
D: FVNQHLCGSHLVEALYLVCGERGFFYTPK
input PDB
Selected Chain(s) A,B,C,D
Distance of aggregation 5 Å
FoldX usage Yes
Dynamic mode No
Automated mutations Yes
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:01:49)
[INFO]       Auto_mut: Residue number 1 from chain B and a score of 2.275 (phenylalanine) selected 
                       for automated muatation                                                     (00:01:51)
[INFO]       Auto_mut: Residue number 1 from chain D and a score of 2.267 (phenylalanine) selected 
                       for automated muatation                                                     (00:01:51)
[INFO]       Auto_mut: Residue number 10 from chain C and a score of 1.989 (isoleucine) selected   
                       for automated muatation                                                     (00:01:51)
[INFO]       Auto_mut: Residue number 10 from chain A and a score of 1.988 (isoleucine) selected   
                       for automated muatation                                                     (00:01:51)
[INFO]       Auto_mut: Residue number 2 from chain B and a score of 1.871 (valine) selected for    
                       automated muatation                                                         (00:01:51)
[INFO]       Auto_mut: Residue number 2 from chain D and a score of 1.831 (valine) selected for    
                       automated muatation                                                         (00:01:51)
[INFO]       Auto_mut: Mutating residue number 1 from chain B (phenylalanine) into glutamic acid   (00:01:51)
[INFO]       Auto_mut: Mutating residue number 1 from chain B (phenylalanine) into aspartic acid   (00:01:51)
[INFO]       Auto_mut: Mutating residue number 1 from chain D (phenylalanine) into glutamic acid   (00:01:51)
[INFO]       Auto_mut: Mutating residue number 1 from chain B (phenylalanine) into lysine          (00:02:47)
[INFO]       Auto_mut: Mutating residue number 1 from chain B (phenylalanine) into arginine        (00:02:48)
[INFO]       Auto_mut: Mutating residue number 1 from chain D (phenylalanine) into lysine          (00:02:51)
[INFO]       Auto_mut: Mutating residue number 1 from chain D (phenylalanine) into aspartic acid   (00:03:50)
[INFO]       Auto_mut: Mutating residue number 10 from chain C (isoleucine) into glutamic acid     (00:03:51)
[INFO]       Auto_mut: Mutating residue number 10 from chain C (isoleucine) into aspartic acid     (00:04:03)
[INFO]       Auto_mut: Mutating residue number 10 from chain C (isoleucine) into lysine            (00:04:45)
[INFO]       Auto_mut: Mutating residue number 1 from chain D (phenylalanine) into arginine        (00:04:45)
[INFO]       Auto_mut: Mutating residue number 10 from chain C (isoleucine) into arginine          (00:04:54)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (isoleucine) into glutamic acid     (00:05:47)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (isoleucine) into aspartic acid     (00:05:50)
[INFO]       Auto_mut: Mutating residue number 2 from chain B (valine) into glutamic acid          (00:05:54)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (isoleucine) into arginine          (00:06:41)
[INFO]       Auto_mut: Mutating residue number 10 from chain A (isoleucine) into lysine            (00:06:42)
[INFO]       Auto_mut: Mutating residue number 2 from chain B (valine) into lysine                 (00:07:00)
[INFO]       Auto_mut: Mutating residue number 2 from chain B (valine) into aspartic acid          (00:07:41)
[INFO]       Auto_mut: Mutating residue number 2 from chain D (valine) into glutamic acid          (00:07:43)
[INFO]       Auto_mut: Mutating residue number 2 from chain D (valine) into aspartic acid          (00:08:20)
[INFO]       Auto_mut: Mutating residue number 2 from chain B (valine) into arginine               (00:08:42)
[INFO]       Auto_mut: Mutating residue number 2 from chain D (valine) into lysine                 (00:08:46)
[INFO]       Auto_mut: Mutating residue number 2 from chain D (valine) into arginine               (00:09:20)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain B (phenylalanine) into       
                       glutamic acid: Energy difference: -0.1404 kcal/mol, Difference in average   
                       score from the base case: -0.0580                                           (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain B (phenylalanine) into       
                       lysine: Energy difference: 0.6604 kcal/mol, Difference in average score     
                       from the base case: -0.0534                                                 (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain B (phenylalanine) into       
                       aspartic acid: Energy difference: -0.5944 kcal/mol, Difference in average   
                       score from the base case: -0.0611                                           (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain B (phenylalanine) into       
                       arginine: Energy difference: 0.4985 kcal/mol, Difference in average score   
                       from the base case: -0.0563                                                 (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain D (phenylalanine) into       
                       glutamic acid: Energy difference: -0.0768 kcal/mol, Difference in average   
                       score from the base case: -0.0592                                           (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain D (phenylalanine) into       
                       lysine: Energy difference: 0.0513 kcal/mol, Difference in average score     
                       from the base case: -0.0529                                                 (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain D (phenylalanine) into       
                       aspartic acid: Energy difference: -0.4952 kcal/mol, Difference in average   
                       score from the base case: -0.0582                                           (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain D (phenylalanine) into       
                       arginine: Energy difference: -0.3334 kcal/mol, Difference in average score  
                       from the base case: -0.0527                                                 (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain C (isoleucine) into         
                       glutamic acid: Energy difference: -0.4777 kcal/mol, Difference in average   
                       score from the base case: -0.0579                                           (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain C (isoleucine) into lysine: 
                       Energy difference: -0.3551 kcal/mol, Difference in average score from the   
                       base case: -0.0561                                                          (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain C (isoleucine) into         
                       aspartic acid: Energy difference: -0.6529 kcal/mol, Difference in average   
                       score from the base case: -0.0603                                           (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain C (isoleucine) into         
                       arginine: Energy difference: -0.8105 kcal/mol, Difference in average score  
                       from the base case: -0.0581                                                 (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: -0.1877 kcal/mol, Difference in average   
                       score from the base case: -0.0601                                           (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.1784 kcal/mol, Difference in average score from the   
                       base case: -0.0588                                                          (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: -0.1586 kcal/mol, Difference in average   
                       score from the base case: -0.0600                                           (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 10 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.1858 kcal/mol, Difference in average score  
                       from the base case: -0.0582                                                 (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain B (valine) into glutamic     
                       acid: Energy difference: -0.8800 kcal/mol, Difference in average score from 
                       the base case: -0.0592                                                      (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain B (valine) into lysine:      
                       Energy difference: -0.5847 kcal/mol, Difference in average score from the   
                       base case: -0.0649                                                          (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain B (valine) into aspartic     
                       acid: Energy difference: -0.8735 kcal/mol, Difference in average score from 
                       the base case: -0.0585                                                      (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain B (valine) into arginine:    
                       Energy difference: -0.2888 kcal/mol, Difference in average score from the   
                       base case: -0.0656                                                          (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain D (valine) into glutamic     
                       acid: Energy difference: -0.7365 kcal/mol, Difference in average score from 
                       the base case: -0.0584                                                      (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain D (valine) into lysine:      
                       Energy difference: -0.7180 kcal/mol, Difference in average score from the   
                       base case: -0.0607                                                          (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain D (valine) into aspartic     
                       acid: Energy difference: -0.9192 kcal/mol, Difference in average score from 
                       the base case: -0.0579                                                      (00:10:29)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain D (valine) into arginine:    
                       Energy difference: -0.4956 kcal/mol, Difference in average score from the   
                       base case: -0.0665                                                          (00:10:29)
[INFO]       Main:     Simulation completed successfully.                                          (00:10:33)
Show buried residues
Minimal score value
-2.0522
Maximal score value
2.2745
Average score
-0.0507
Total score value
-5.0697
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
1 G A -0.4663
2 I A 0.0000
3 V A -0.1196
4 E A -1.9825
5 Q A -1.4276
6 C A 0.0000
7 C A 0.1598
8 T A -0.0782
9 S A 0.1416
10 I A 1.9880
11 C A 0.4306
12 S A 0.2109
13 L A 1.7707
14 Y A 1.4574
15 Q A -0.5304
16 L A 0.0000
17 E A -1.2030
18 N A -1.3651
19 Y A 0.2441
20 C A -0.0607
21 N A -1.2565
1 F B 2.2745
2 V B 1.8709
3 N B -0.8326
4 Q B -0.9242
5 H B -0.3478
6 L B 1.2590
7 C B 0.3299
8 G B 0.0000
9 S B -0.2105
10 H B -0.9956
11 L B 0.0000
12 V B 0.0000
13 E B -0.3914
14 A B -0.0607
15 L B 0.0000
16 Y B 0.4238
17 L B 1.6160
18 V B 0.5171
19 C B 0.0000
20 G B -0.5889
21 E B -2.0329
22 R B -1.2353
23 G B 0.0000
24 F B 0.0000
25 F B 1.7001
26 Y B 0.0000
27 T B -0.0677
28 P B -0.3810
29 K B -1.7108
1 G C -0.4663
2 I C 0.0000
3 V C -0.1200
4 E C -1.9709
5 Q C -1.3550
6 C C 0.0000
7 C C 0.1728
8 T C -0.0762
9 S C 0.1429
10 I C 1.9888
11 C C 0.4297
12 S C 0.1593
13 L C 1.7655
14 Y C 1.4651
15 Q C -0.4902
16 L C 0.0000
17 E C -1.2739
18 N C -1.4398
19 Y C -0.0839
20 C C 0.0000
21 N C -1.2730
1 F D 2.2665
2 V D 1.8310
3 N D -1.0513
4 Q D -0.8790
5 H D -0.2887
6 L D 1.2123
7 C D 0.3386
8 G D 0.0000
9 S D -0.2223
10 H D -0.9976
11 L D 0.0000
12 V D 0.0000
13 E D -0.5498
14 A D -0.0876
15 L D 0.0000
16 Y D 0.4176
17 L D 1.6462
18 V D 0.6874
19 C D 0.0000
20 G D -0.5762
21 E D -2.0522
22 R D -1.3436
23 G D 0.0000
24 F D 0.0000
25 F D 1.0027
26 Y D 0.0000
27 T D -0.0331
28 P D -0.3788
29 K D -1.7118
Download PDB file
View in 3Dmol
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Automated mutations analysis

In the automated mutations mode, the server selects aggregation prone resides and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine. The table below shows 2 best scored mutants for each mutated residue. Protein variants are ordered according to the mutation effect they had on protein stability (energetic effect) together with the difference in the average per-residue aggregation score between the wild type and the mutant (in the table green values indicate a positive change, grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this CSV file.

Mutant
Energetic effect
Score comparison
VD2D -0.9192 -0.0579 View CSV PDB
VE2B -0.88 -0.0592 View CSV PDB
VD2B -0.8735 -0.0585 View CSV PDB
IR10C -0.8105 -0.0581 View CSV PDB
VK2D -0.718 -0.0607 View CSV PDB
ID10C -0.6529 -0.0603 View CSV PDB
FD1B -0.5944 -0.0611 View CSV PDB
FD1D -0.4952 -0.0582 View CSV PDB
FR1D -0.3334 -0.0527 View CSV PDB
IE10A -0.1877 -0.0601 View CSV PDB
IR10A -0.1858 -0.0582 View CSV PDB
FE1B -0.1404 -0.058 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018